This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We compare methods of data-dependent acquisition (DDA) and data-independent acquisition (DIA), implemented both on a traditional LTQ and an LTQ equipped with an electrodynamic ion funnel.